#!/bin/sh

# run from directory where this script is
cd `dirname $0`
EXAMPLE_DIR=`pwd`

# check whether echo has the -e option
if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi

$ECHO
$ECHO "$EXAMPLE_DIR : starting"
$ECHO
$ECHO "This example shows how to use cp.x to perform molecular dynamics"
$ECHO "simulation of SiO2."

# set the needed environment variables
. ../../../environment_variables

# required executables and pseudopotentials
BIN_LIST="cp.x"
PSEUDO_LIST="Si.pz-vbc.UPF O.pz-rrkjus.UPF"

$ECHO
$ECHO "  executables directory: $BIN_DIR"
$ECHO "  pseudo directory:      $PSEUDO_DIR"
$ECHO "  temporary directory:   $TMP_DIR"
$ECHO "  checking that needed directories and files exist...\c"

# check for directories
for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do
    if test ! -d $DIR ; then
        $ECHO
        $ECHO "ERROR: $DIR not existent or not a directory"
        $ECHO "Aborting"
        exit 1
    fi
done
for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do
    if test ! -d $DIR ; then
        mkdir $DIR
    fi
done
cd $EXAMPLE_DIR/results

# check for executables
for FILE in $BIN_LIST ; do
    if test ! -x $BIN_DIR/$FILE ; then
        $ECHO
        $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable"
        $ECHO "Aborting"
        exit 1
    fi
done

# check for pseudopotentials
for FILE in $PSEUDO_LIST ; do
    if test ! -r $PSEUDO_DIR/$FILE ; then
       $ECHO
       $ECHO "Downloading $FILE to $PSEUDO_DIR...\c"
            $WGET $PSEUDO_DIR/$FILE $NETWORK_PSEUDO/$FILE 2> /dev/null
    fi
    if test $? != 0; then
        $ECHO
        $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"
        $ECHO "Aborting"
        exit 1
    fi
done
$ECHO " done"

# how to run executables
CP_COMMAND="$PARA_PREFIX $BIN_DIR/cp.x $PARA_POSTFIX"
$ECHO
$ECHO "  running cp.x as: $CP_COMMAND"
$ECHO

# clean TMP_DIR
$ECHO "  cleaning $TMP_DIR...\c"
rm -rf $TMP_DIR/cp*
$ECHO " done"

# molecular dynamics calculation
cat >  sio2.cp.start.in << EOF
 &control
    calculation='cp',
    restart_mode='from_scratch',
    nstep=20, iprint=20, isave=20,
    dt=5.0,
    ndr=90, ndw=91,
    pseudo_dir='$PSEUDO_DIR/',
    outdir='$TMP_DIR/',
 /
 &system
    ibrav=8, celldm(1)=9.28990, celldm(2)=1.73206, celldm(3)=1.09955,
    nat=18, ntyp=2, nbnd=48, nspin=1,
    ecutwfc=20.0, ecutrho=150.0,
    nr1b=16, nr2b=16, nr3b=16,
    qcutz=150., q2sigma=2.0, ecfixed=16.0,
 /
 &electrons
    electron_dynamics='damp', electron_damping=0.2,
    startingwfc='random', ampre=0.01,
    emass=700., emass_cutoff=3.,
 /
 &ions
    ion_dynamics='none',
    ion_radius(1)=1.0, ion_radius(2)=1.0,
 /
ATOMIC_SPECIES
   O  16.00 O.pz-rrkjus.UPF
  Si  28.00 Si.pz-vbc.UPF
ATOMIC_POSITIONS bohr
 O  3.18829368  14.83237039   1.22882961
 O  7.83231469   6.78704039   1.22882961
 O  2.07443467   5.99537992   4.73758250
 O  6.72031366  14.04231898   4.73758250
 O  3.96307134  11.26989826   7.87860582
 O  8.60802134   3.22295920   7.87860582
 O  3.96307134   4.81915267   9.14625133
 O  8.60802134  12.86448267   9.14625133
 O  3.18736469   1.25668055   5.58029607
 O  7.83324368   9.30201055   5.58029607
 O  2.07536366  10.09206195   2.07358613
 O  6.71938467   2.04673195   2.07358613
Si  0.28891589   8.04533000   3.40456284
Si  4.93386589   0.00000000   3.40456284
Si  2.13389003  12.27717358  -0.04188031
Si  6.77884003   4.23184358  -0.04188031
Si  2.13389003   3.81348642   6.85202747
Si  6.77884003  11.85881642   6.85202747
EOF
$ECHO "  running the calculation with fixed ions...\c"
$CP_COMMAND < sio2.cp.start.in > sio2.cp.start.out
check_failure $?
$ECHO " done"

# molecular dynamics calculation
cat > sio2.cp.restart.in << EOF
 &control
    calculation='cp',
    restart_mode='reset_counters',
    nstep=50, iprint=50, isave=50,
    dt=15.0,
    ndr=91, ndw=92,
    pseudo_dir='$PSEUDO_DIR/',
    outdir='$TMP_DIR/',
 /
 &system
    ibrav=8, celldm(1)=9.28990, celldm(2)=1.73206, celldm(3)=1.09955,
    nat=18, ntyp=2, nbnd=48, nspin=1,
    ecutwfc=20.0, ecutrho=150.0,
    nr1b=16, nr2b=16, nr3b=16,
    qcutz=150., q2sigma=2.0, ecfixed=16.0,
 /
 &electrons
    electron_dynamics='damp', electron_damping=0.2,
    emass=700., emass_cutoff=3.,
 /
 &ions
    ion_dynamics='none',
    ion_radius(1)=1.0, ion_radius(2)=1.0,
 /
ATOMIC_SPECIES
   O  16.00 O.pz-rrkjus.UPF
  Si  28.00 Si.pz-vbc.UPF
ATOMIC_POSITIONS bohr
 O  3.18829368  14.83237039   1.22882961
 O  7.83231469   6.78704039   1.22882961
 O  2.07443467   5.99537992   4.73758250
 O  6.72031366  14.04231898   4.73758250
 O  3.96307134  11.26989826   7.87860582
 O  8.60802134   3.22295920   7.87860582
 O  3.96307134   4.81915267   9.14625133
 O  8.60802134  12.86448267   9.14625133
 O  3.18736469   1.25668055   5.58029607
 O  7.83324368   9.30201055   5.58029607
 O  2.07536366  10.09206195   2.07358613
 O  6.71938467   2.04673195   2.07358613
Si  0.28891589   8.04533000   3.40456284
Si  4.93386589   0.00000000   3.40456284
Si  2.13389003  12.27717358  -0.04188031
Si  6.77884003   4.23184358  -0.04188031
Si  2.13389003   3.81348642   6.85202747
Si  6.77884003  11.85881642   6.85202747
EOF
$ECHO "  running the calculation with fixed ions, restart...\c"
$CP_COMMAND < sio2.cp.restart.in > sio2.cp.restart.out
check_failure $?
$ECHO " done"

# molecular dynamics calculation
cat > sio2.vc-cp.in << EOF
 &control
    calculation='vc-cp',
    restart_mode='reset_counters',
    nstep=10, iprint=10, isave=10,
    dt=12.0,
    ndr=92, ndw=93,
    pseudo_dir='$PSEUDO_DIR/',
    outdir='$TMP_DIR/',
 /
 &system
    ibrav=8, celldm(1)=9.28990, celldm(2)=1.73206, celldm(3)=1.09955,
    nat=18, ntyp=2, nbnd=48, nspin=1,
    ecutwfc=20.0, ecutrho=150.0,
    nr1b=16, nr2b=16, nr3b=16,
    qcutz=150., q2sigma=2.0, ecfixed=16.0,
 /
 &electrons
    electron_dynamics='verlet', ortho_max=30,
    emass=700., emass_cutoff=3.,
 /
 &ions
    ion_dynamics='verlet', ion_temperature='nose',
    tempw=300, fnosep=6.6666,
    ion_radius(1)=1.0, ion_radius(2)=1.0,
 /
 &cell
    cell_dynamics='pr', cell_temperature='nose',
    temph=300., fnoseh=8.6071, press=1.0,
 /
ATOMIC_SPECIES
   O  16.00 O.pz-rrkjus.UPF
  Si  28.00 Si.pz-vbc.UPF
ATOMIC_POSITIONS bohr
 O  3.18829368  14.83237039   1.22882961
 O  7.83231469   6.78704039   1.22882961
 O  2.07443467   5.99537992   4.73758250
 O  6.72031366  14.04231898   4.73758250
 O  3.96307134  11.26989826   7.87860582
 O  8.60802134   3.22295920   7.87860582
 O  3.96307134   4.81915267   9.14625133
 O  8.60802134  12.86448267   9.14625133
 O  3.18736469   1.25668055   5.58029607
 O  7.83324368   9.30201055   5.58029607
 O  2.07536366  10.09206195   2.07358613
 O  6.71938467   2.04673195   2.07358613
Si  0.28891589   8.04533000   3.40456284
Si  4.93386589   0.00000000   3.40456284
Si  2.13389003  12.27717358  -0.04188031
Si  6.77884003   4.23184358  -0.04188031
Si  2.13389003   3.81348642   6.85202747
Si  6.77884003  11.85881642   6.85202747
EOF
$ECHO "  running the variable-cell calculation...\c"
$CP_COMMAND < sio2.vc-cp.in > sio2.vc-cp.out
check_failure $?
$ECHO " done"

# molecular dynamics calculation
cat > sio2.vc-cp.restart.in << EOF
 &control
    calculation='vc-cp',
    restart_mode='reset_counters',
    nstep=10, iprint=10, isave=10,
    dt=12.0,
    ndr=93, ndw=94,
    pseudo_dir='$PSEUDO_DIR/',
    outdir='$TMP_DIR/',
 /
 &system
    ibrav=8, celldm(1)=9.28990, celldm(2)=1.73206, celldm(3)=1.09955,
    nat=18, ntyp=2, nbnd=48, nspin=1,
    ecutwfc=20.0, ecutrho=150.0,
    nr1b=16, nr2b=16, nr3b=16,
    qcutz=150., q2sigma=2.0, ecfixed=16.0,
 /
 &electrons
    electron_dynamics='verlet', ortho_max=30,
    emass=700., emass_cutoff=3.,
 /
 &ions
    ion_dynamics='verlet', ion_temperature='nose',
    tempw=300, fnosep=6.6666,
    ion_radius(1)=1.0, ion_radius(2)=1.0,
 /
 &cell
    cell_dynamics='pr', cell_temperature='nose',
    temph=300., fnoseh=8.6071, press=1.0,
 /
ATOMIC_SPECIES
   O  16.00 O.pz-rrkjus.UPF
  Si  28.00 Si.pz-vbc.UPF
ATOMIC_POSITIONS bohr
 O  3.18829368  14.83237039   1.22882961
 O  7.83231469   6.78704039   1.22882961
 O  2.07443467   5.99537992   4.73758250
 O  6.72031366  14.04231898   4.73758250
 O  3.96307134  11.26989826   7.87860582
 O  8.60802134   3.22295920   7.87860582
 O  3.96307134   4.81915267   9.14625133
 O  8.60802134  12.86448267   9.14625133
 O  3.18736469   1.25668055   5.58029607
 O  7.83324368   9.30201055   5.58029607
 O  2.07536366  10.09206195   2.07358613
 O  6.71938467   2.04673195   2.07358613
Si  0.28891589   8.04533000   3.40456284
Si  4.93386589   0.00000000   3.40456284
Si  2.13389003  12.27717358  -0.04188031
Si  6.77884003   4.23184358  -0.04188031
Si  2.13389003   3.81348642   6.85202747
Si  6.77884003  11.85881642   6.85202747
EOF

$ECHO "  running the variable-cell calculation, restart...\c"
$CP_COMMAND < sio2.vc-cp.restart.in >  sio2.vc-cp.restart.out
check_failure $?
$ECHO " done"

$ECHO
$ECHO "$EXAMPLE_DIR : done"
